[FEAT] - log transformation server logic

NAMESPACE

@@ -11,6 +11,7 @@ importFrom(MultiAssayExperiment,getWithColData)
 importFrom(QFeatures,QFeatures)
 importFrom(QFeatures,addAssayLink)
 importFrom(QFeatures,filterFeatures)
+importFrom(QFeatures,logTransform)
 importFrom(QFeatures,readQFeatures)
 importFrom(QFeatures,zeroIsNA)
 importFrom(RColorBrewer,brewer.pal)

R/interface_module_log_transform_tab.R

@@ -27,28 +27,7 @@ interface_module_log_transform_tab <- function(id) {
             ),
             trigger = "hover"
         ),
-        interface_box_distribution("box_distribution"),
-        actionButton(
-            NS(id, "export"),
-            "Save the processed assays",
-            icon("hand-pointer", class = "fa-solid"),
-            width = "100%",
-            class = "load-button"
-        ),
-        shinyBS::bsTooltip(
-            id = NS(id, "export"),
-            title = paste("Write the processed assays to the QFeatures object.",
-                "This is needed to proceed to the next steps.",
-                sep = " "
-            ),
-            trigger = "hover",
-            placement = "top"
-        )
-    )
-}
-
-interface_box_distribution <- function(id) {
-    box(
+        box(
         title = "Log Transformation",
         status = "primary",
         width = 12,
@@ -87,8 +66,31 @@ interface_box_distribution <- function(id) {
                     label = "Log Base",
                     choices = c(2, 10),
                     selected = 2
+                ),
+                numericInput(inputId = NS(id, "pseudocount"),
+                    label = "Pseudocount",
+                    value = 0,
+                    min = 0,
+                    step = 1
                 )
             )
         )
+    ),
+        actionButton(
+            NS(id, "export"),
+            "Save the processed assays",
+            icon("hand-pointer", class = "fa-solid"),
+            width = "100%",
+            class = "load-button"
+        ),
+        shinyBS::bsTooltip(
+            id = NS(id, "export"),
+            title = paste("Write the processed assays to the QFeatures object.",
+                "This is needed to proceed to the next steps.",
+                sep = " "
+            ),
+            trigger = "hover",
+            placement = "top"
+        )
     )
 }

R/server_module_log_transform_tab.R

@@ -10,6 +10,39 @@
 #'
 server_module_log_transform_tab <- function(id, step_number) {
     moduleServer(id, function(input, output, session) {
-        return(NULL)
+        assays_to_process <- eventReactive(input$reload, {
+            error_handler(page_assays_subset,
+                component_name = "Page assays subset",
+                qfeatures = global_rv$qfeatures,
+                pattern = paste0("_(QFeaturesGUI#", step_number - 1, ")")
+            )
+        })
+
+        processed_assays <- reactive({
+            req(assays_to_process())
+            error_handler(
+                log_transform_qfeatures,
+                component_name = "Log transformation",
+                qfeatures = assays_to_process(),
+                base = as.integer(input$log_base),
+                pseudocount = as.integer(input$pseudocount)
+            )
+        })
+
+        observeEvent(input$export, {
+            req(processed_assays())
+            loading(paste("Be aware that this operation",
+                "can be quite time consuming for large data sets",
+                sep = " "
+            ))
+            error_handler(
+                add_assays_to_global_rv,
+                component_name = "Add assays to global_rv",
+                processed_qfeatures = processed_assays(),
+                step_number = step_number,
+                type = "log_transformation"
+            )
+            removeModal()
+        })
     })
     }

R/utils_global.R

@@ -339,3 +339,24 @@ add_assays_to_global_rv <- function(processed_qfeatures, step_number, type) {
         )
     }
 }
+
+
+#' A function that will logTransform all the assays of a qfeatures
+#' @param qfeatures `QFeatures` object to logTransform
+#' @param base `numeric` base of the log transformation
+#' @param pseudocount `numeric` pseudocount to add to the data
+#' @return `QFeatures` object with the log transformed assays
+#' @rdname INTERNAL_log_transform_qfeatures
+#' @keywords internal
+#' @importFrom QFeatures logTransform QFeatures colData
+#' 
+
+log_transform_qfeatures <- function(qfeatures, base, pseudocount) {
+    el <- lapply(names(qfeatures), function(name) {
+        QFeatures::logTransform(object = qfeatures[[name]],
+            base = base,
+            pc = pseudocount)
+    })
+    names(el) <- names(qfeatures)
+    QFeatures(el, colData = colData(qfeatures))
+    }